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Items: 1 to 20 of 85

1.

Differential analysis of gene regulation at transcript resolution with RNA-seq.

Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L.

Nat Biotechnol. 2013 Jan;31(1):46-53. doi: 10.1038/nbt.2450. Epub 2012 Dec 9.

2.

Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS.

Park JW, Tokheim C, Shen S, Xing Y.

Methods Mol Biol. 2013;1038:171-9. doi: 10.1007/978-1-62703-514-9_10.

PMID:
23872975
3.

rSeqDiff: detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test.

Shi Y, Jiang H.

PLoS One. 2013 Nov 18;8(11):e79448. doi: 10.1371/journal.pone.0079448. eCollection 2013.

4.

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.

Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J.

Nucleic Acids Res. 2013 Jan;41(2):e39. doi: 10.1093/nar/gks1026. Epub 2012 Nov 15.

5.

Towards reliable isoform quantification using RNA-SEQ data.

Howard BE, Heber S.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S6. doi: 10.1186/1471-2105-11-S3-S6.

6.

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level.

Zheng S, Chen L.

Nucleic Acids Res. 2009 Jun;37(10):e75. doi: 10.1093/nar/gkp282. Epub 2009 May 5.

7.

A survey of software for genome-wide discovery of differential splicing in RNA-Seq data.

Hooper JE.

Hum Genomics. 2014 Jan 21;8:3. doi: 10.1186/1479-7364-8-3.

8.

Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq.

Beane J, Vick J, Schembri F, Anderlind C, Gower A, Campbell J, Luo L, Zhang XH, Xiao J, Alekseyev YO, Wang S, Levy S, Massion PP, Lenburg M, Spira A.

Cancer Prev Res (Phila). 2011 Jun;4(6):803-17. doi: 10.1158/1940-6207.CAPR-11-0212.

9.

Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching.

Rehrauer H, Opitz L, Tan G, Sieverling L, Schlapbach R.

BMC Bioinformatics. 2013 Dec 24;14:370. doi: 10.1186/1471-2105-14-370.

10.

Global gene expression response of a population exposed to benzene: a pilot study exploring the use of RNA-sequencing technology.

Thomas R, McHale CM, Lan Q, Hubbard AE, Zhang L, Vermeulen R, Li G, Rappaport SM, Yin S, Rothman N, Smith MT.

Environ Mol Mutagen. 2013 Aug;54(7):566-73. doi: 10.1002/em.21801. Epub 2013 Aug 1.

11.

LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data.

Lin B, Zhang LF, Chen X.

BMC Genomics. 2014;15 Suppl 10:S7. doi: 10.1186/1471-2164-15-S10-S7. Epub 2014 Dec 12.

12.

The bench scientist's guide to statistical analysis of RNA-Seq data.

Yendrek CR, Ainsworth EA, Thimmapuram J.

BMC Res Notes. 2012 Sep 14;5:506. doi: 10.1186/1756-0500-5-506.

13.

An Island-Based Approach for Differential Expression Analysis.

Eteleeb AM, Flight RM, Harrison BJ, Petruska JC, Rouchka EC.

ACM Conf Bioinform Comput Biol Biomed Inform (2013). 2013 Dec 31;2013:419-429.

14.

Identifying differentially expressed transcripts from RNA-seq data with biological variation.

Glaus P, Honkela A, Rattray M.

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.

15.

Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level.

Farajzadeh L, Hornshøj H, Momeni J, Thomsen B, Larsen K, Hedegaard J, Bendixen C, Madsen LB.

Biochem Biophys Res Commun. 2013 Aug 23;438(2):346-52. doi: 10.1016/j.bbrc.2013.07.074. Epub 2013 Jul 27.

16.

A generalized dSpliceType framework to detect differential splicing and differential expression events using RNA-Seq.

Zhu D, Deng N, Bai C.

IEEE Trans Nanobioscience. 2015 Mar;14(2):192-202. doi: 10.1109/TNB.2015.2388593. Epub 2015 Feb 11.

PMID:
25680210
17.

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools.

Leshkowitz D, Feldmesser E, Friedlander G, Jona G, Ainbinder E, Parmet Y, Horn-Saban S.

PLoS One. 2016 Apr 21;11(4):e0153782. doi: 10.1371/journal.pone.0153782. eCollection 2016.

18.

The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.

Atallah J, Plachetzki DC, Jasper WC, Johnson BR.

PLoS One. 2013 Dec 16;8(12):e84160. doi: 10.1371/journal.pone.0084160. eCollection 2013.

19.

Unproductive alternative splicing and nonsense mRNAs: a widespread phenomenon among plant circadian clock genes.

Filichkin SA, Mockler TC.

Biol Direct. 2012 Jul 2;7:20. doi: 10.1186/1745-6150-7-20.

20.

Bias detection and correction in RNA-Sequencing data.

Zheng W, Chung LM, Zhao H.

BMC Bioinformatics. 2011 Jul 19;12:290. doi: 10.1186/1471-2105-12-290.

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